Merge branch '1960-fix-install-tests' into 'master'

Resolve "fix install tests"

Closes #1960

See merge request !1655

.gitlab-ci.yml

@@ -480,7 +480,7 @@ test_install_debian_package:
      - echo "deb http://archive.debian.org/debian-security stretch/updates main" >> /etc/apt/sources.list
      - echo "deb-src http://archive.debian.org/debian-security stretch/updates main" >> /etc/apt/sources.list
      - apt-get update
-     - DEBIAN_FRONTEND=noninteractive apt-get install -y ssh software-properties-common dirmngr wget curl postgresql
+     - DEBIAN_FRONTEND=noninteractive apt-get install -y ssh software-properties-common dirmngr wget curl postgresql screen
      - service postgresql start
      - debian_file=$(ls debian/*.deb)
      - echo debconf minerva/internal/skip-preseed boolean true | debconf-set-selections
@@ -489,46 +489,15 @@ test_install_debian_package:
      - echo debconf minerva/remote/host select localhost | debconf-set-selections
      - echo debconf minerva/db/dbname select minerva_db | debconf-set-selections
      - echo debconf minerva/db/app-user select minerva_user@localhost | debconf-set-selections
-     - apt-get update
      - DEBIAN_FRONTEND=noninteractive apt-get install -y ./$debian_file
-     - java -jar /usr/share/minerva/minerva.jar &
-#we need to wait a bit for tomcat start
+     - screen -d -m java -jar /usr/share/minerva/minerva.jar
+#we need to wait a bit - app needs to start
      - sleep 15
      - wget http://localhost:8080/minerva/
 #test if we can login and list projects
      - test 200 = $(curl -X POST -d "login=admin&password=admin" --write-out %{http_code} --silent --output /dev/null -c cookie.txt http://localhost:8080/minerva/api/doLogin)
      - test 200 = $(curl --write-out %{http_code} --silent --output /dev/null --cookie cookie.txt http://localhost:8080/minerva/api/projects/)
 
-test_deploy_with_db_without_superadmin_rights:
-  image: maven:3.8.6-jdk-8
-  stage: test
-  services:
-    - postgres:9.6
-  dependencies:
-    - build_jar
-  tags:
-    - privileged
-  only:
-    - tags
-  script:
-    - apt-get update
-    - DEBIAN_FRONTEND=noninteractive apt-get install -y postgresql-client
-    - mkdir -p /etc/minerva
-    - echo "database.uri=jdbc:postgresql://postgres:5432/test" > /etc/minerva/db.properties
-    - echo "database.username=test" >> /etc/minerva/db.properties
-    - echo "database.password=test" >> /etc/minerva/db.properties
-    - echo "CREATE DATABASE test;CREATE USER test WITH ENCRYPTED PASSWORD 'test';GRANT ALL PRIVILEGES ON DATABASE test TO test;" >tmp.sql
-    - PGPASSWORD=$POSTGRES_PASSWORD psql -h postgres -U $POSTGRES_USER $POSTGRES_DB < tmp.sql
-    - mkdir -p /usr/share/minerva/data/
-    - mv minerva.jar /usr/share/minerva/
-    - java -jar /usr/share/minerva/minerva.jar
-    - sleep 15
-    - curl http://localhost:8080/minerva/
-#test if we can login and list projects
-    - test 200 = $(curl -X POST -d "login=admin&password=admin" --write-out %{http_code} --silent --output /dev/null -c cookie.txt http://localhost:8080/minerva/api/doLogin)
-    - test 200 = $(curl --write-out %{http_code} --silent --output /dev/null --cookie cookie.txt http://localhost:8080/minerva/api/projects/)
-
-
 .test_database_template: &test_database_definition
   image: maven:3.8.6-jdk-8
   stage: test

CHANGELOG

@@ -7,6 +7,9 @@ minerva (17.0.0~beta.1) unstable; urgency=medium
     account disabled (#1635)
   * Bug fix (regression): accepting ToS was impossible (#1974)
   * Bug fix (regression): export page did not work (#1965)
+  * Bug fix: refresh of DAPI data did not work properly (#1967)
+  * Bug fix: download genomes stopped working (http://hgdownload.cse.ucsc.edu/
+    is down)
   * Bug fix: upload of invalid javascript plugin was throwing exception
     (#1964)
 

annotation/src/main/java/lcsb/mapviewer/annotation/services/dapi/DapiConnectorImpl.java

@@ -64,7 +64,7 @@ public class DapiConnectorImpl extends CachableInterface implements DapiConnecto
   }
 
   public DapiConnectorImpl(final ConfigurationDao configurationDao) {
-    super(DapiConnectorImpl.class);
+    super(DapiConnector.class);
     this.configurationDao = configurationDao;
   }
 

annotation/src/test/java/lcsb/mapviewer/annotation/cache/GeneralCacheTest.java

 package lcsb.mapviewer.annotation.cache;
 
+import static org.junit.Assert.assertEquals;
 import static org.junit.Assert.assertNotNull;
 import static org.junit.Assert.assertNull;
 import static org.junit.Assert.assertTrue;
@@ -10,9 +11,14 @@ import org.junit.Test;
 import org.springframework.beans.factory.annotation.Autowired;
 
 import lcsb.mapviewer.annotation.AnnotationTestFunctions;
+import lcsb.mapviewer.annotation.services.ModelAnnotator;
 import lcsb.mapviewer.annotation.services.PubmedParser;
+import lcsb.mapviewer.annotation.services.dapi.DapiConnector;
 import lcsb.mapviewer.common.exception.InvalidArgumentException;
 import lcsb.mapviewer.model.cache.CacheType;
+import lcsb.mapviewer.model.job.MinervaJob;
+import lcsb.mapviewer.model.job.MinervaJobPriority;
+import lcsb.mapviewer.model.job.MinervaJobType;
 
 public class GeneralCacheTest extends AnnotationTestFunctions {
 
@@ -22,6 +28,9 @@ public class GeneralCacheTest extends AnnotationTestFunctions {
   @Autowired
   private GeneralCacheInterface databaseLevelCache;
 
+  @Autowired
+  private DapiConnector dapiConnector;
+
   @Before
   public void setUp() throws Exception {
   }
@@ -84,4 +93,12 @@ public class GeneralCacheTest extends AnnotationTestFunctions {
     }
   }
 
+  @Test
+  public void testExecute() throws Exception {
+    CacheQueryMinervaJob parameters = new CacheQueryMinervaJob("https://google.com/",
+        ((CachableInterface) ModelAnnotator.unwrapProxy(dapiConnector)).getCacheType().getId());
+    cache.execute(new MinervaJob(MinervaJobType.REFRESH_CACHE, MinervaJobPriority.MEDIUM, parameters));
+    assertEquals(0, super.getErrors().size());
+  }
+
 }

annotation/src/test/java/lcsb/mapviewer/annotation/services/dapi/DapiConnectorImplTest.java

@@ -10,7 +10,7 @@ import org.junit.Test;
 public class DapiConnectorImplTest {
 
   @Test
-  public void testGetLAtestVersion() {
+  public void testGetLatestVersion() {
     DapiConnectorImpl connector = new DapiConnectorImpl(null);
     String version = connector.getLatestVersion(Arrays.asList("2.2", "3.3", "11.2", "10"));
     assertEquals("11.2", version);

persist/src/main/resources/db/migration/hsql/17.0.0~beta.1/V17.0.0.20240208__dapi_cache_with_invalid_class.sql

+update cache_type_table set class_name ='lcsb.mapviewer.annotation.services.dapi.DapiConnector' where class_name='lcsb.mapviewer.annotation.services.dapi.DapiConnectorImpl';
\ No newline at end of file

persist/src/main/resources/db/migration/postgres/17.0.0~beta.1/V17.0.0.20240208__dapi_cache_with_invalid_class.sql

+update cache_type_table set class_name ='lcsb.mapviewer.annotation.services.dapi.DapiConnector' where class_name='lcsb.mapviewer.annotation.services.dapi.DapiConnectorImpl';
\ No newline at end of file